MolNFT v1 · #70937 · protein
Crystal structure of DPH2 from pyrococcus horikoshii with 4FE-4S cluster
3LZD: “Crystal structure of DPH2 from pyrococcus horikoshii with 4FE-4S cluster”. X-ray diffraction, 2 ligands (SF4, SO4), 3 pockets (best druggability 0.78). MolNFT v1 #70937 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3LZD
- Type
- protein
- Length
- 677 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DPH2
- UniProt
- O58832
- Ligands
- SF4, SO4
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DPH2 | protein | 340 | 33% helix, 20% strand | O58832 |
| B | DPH2 | protein | 337 | 34% helix, 21% strand | O58832 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 625 | 0.78 | 0.84 | 77 | SF4, SO4 |
| 2 | 403 | 0.68 | 0.80 | 47 | SF4, SO4 |
| 3 | 58 | 0.38 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1776 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 3LZD · Crystal structure of Dph2 from Pyrococcus horikoshii with 4Fe-4S cluster · the same entry in another collection · chain A against A, TM-score 1.00
- O58832 · AlphaFold monomer V2.0 prediction for 2-(3-amino-3-CARBOXYPROPYL)HISTIDINE synthase… · a predicted model of the same protein · chain B against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O58832
- Elsewhere: RCSB PDB 3LZD · PDBe 3LZD · UniProt O58832
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